Ok I am trying to use the GROMOS96 43a1 force field to run a simulation of a finite CNT. I believe I have figured out how this force field can be modified. I have made the following additions to the respective 43a1 force field files and placed them in the root directory of the simulation:
##################################### ******************* ffG43a1bon.itp ******************* #define gb_48 0.142100 4.7890e+06 ; C - C #define ga_47 120.00 397.48 ; C - C - C ******************* ffG43a1.rtp ******************* [ UNK ] [ atoms ] [ bonds ] C C gb_48 [ angles ] C C C ga_47 [ impropers ] C C C 0 ga_1 ******************* ffG43a1.n2t ******************* C C 1 C ; CNT Carbon with one bond C C 2 C C : CNT double bonded Carbon ##################################### Note I also made the following change to ffG43a1bon.itp (the original line was): #define gd_1 180.000 5.86 2 ; -C-C- 1.4 Now it is: #define gd_1 167.360 5.86 2 ; -C-C- 1.4 I still get the following errors when I run grompp(here is the first 10): ***************************************************** WARNING 1 [file "SWNT_6_6_144.top", line 167]: No default Bond types, using zeroes WARNING 2 [file "SWNT_6_6_144.top", line 167]: No default Bond types for perturbed atoms, using normal values WARNING 3 [file "SWNT_6_6_144.top", line 168]: No default Bond types, using zeroes WARNING 4 [file "SWNT_6_6_144.top", line 168]: No default Bond types for perturbed atoms, using normal values WARNING 5 [file "SWNT_6_6_144.top", line 169]: No default Bond types, using zeroes WARNING 6 [file "SWNT_6_6_144.top", line 169]: No default Bond types for perturbed atoms, using normal values WARNING 7 [file "SWNT_6_6_144.top", line 170]: No default Bond types, using zeroes WARNING 8 [file "SWNT_6_6_144.top", line 170]: No default Bond types for perturbed atoms, using normal values WARNING 9 [file "SWNT_6_6_144.top", line 171]: No default Bond types, using zeroes WARNING 10 [file "SWNT_6_6_144.top", line 171]: No default Bond types for perturbed atoms, using normal values ***************************************************** At http://cs86.com/CNSE/CNT_FFOpt0.zip a zip file with all the files I use can be obtained, and the grompp command I use is: grompp -f md_200k.mdp -c SWNT_6_6_144_b4em.gro -p SWNT_6_6_144.top -maxwarn 10 -pp Also note I am working off the modifications I made to the Gromacs FF and they are as follows: ***************************************************** ffgmx.n2t and add the following 2 lines: C C 1 C ; CNT Carbon with one bond C C 2 C C ; CNT double bonded Carbon ffgmxbon.itp add the following line to it: *** To be very clear about this the first two lines are just telling what section to add it to in the file and what the units of that addition reprsent.*** ##################################### [ bondtypes ] ; i j func b0 kb C C 1 0.14210 478900. ##################################### [ angletypes ] ; i j k func th0 cth C C C 1 120.000 397.480 ##################################### [ dihedraltypes ] ; i l func q0 cq C C 1 0.000 167.360 ##################################### ***************************************************** Thank you very much for your help! ~Christopher Stiles College of Nanoscale Science and Engineering (CNSE) State University of New York, Albany, New York 12203, USA
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